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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ), 'gf_id' => 'HOM05D001276', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001276' ), 'data_identifier' => 'HOM05D001276', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001276', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '492', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33960' => 'bna', 'A03p55720' => 'bna', 'A05p42560' => 'bna', 'A09p05160' => 'bna', 'A09p19430' => 'bna', 'Aa31LG11G8940' => 'aar', 'Aa31LG2G12150' => 'aar', 'Aa31LG5G15410' => 'aar', 'Aa31LG7G10620' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2242' => 'aag', 'Actinidia00055' => 'ach', 'Actinidia23435' => 'ach', 'Actinidia26008' => 'ach', 'Actinidia31159' => 'ach', 'Actinidia36838' => 'ach', 'Actinidia40220' => 'ach', 'Ah.04g160030' => 'amhyb', 'Ah.06g192920' => 'amhyb', 'AL1G65020' => 'aly', 'AL1G65060' => 'aly', 'AL3G15390' => 'aly', 'AL6G40000' => 'aly', 'AL7G28090' => 'aly', 'Aqoxy2G03126' => 'aox', 'Aqoxy3G01847' => 'aox', 'Aqoxy5G00621' => 'aox', 'Aqoxy7G00989' => 'aox', 'arahy.Tifrunner.gnm1.ann1.EA8RPB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FL5QND' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2VJYT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NR0MD6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3NUW0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5YSLN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UWF8Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X0XPJN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XM9QK1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z9XA8H' => 'arhy', 'AT1G54580' => 'ath', 'AT1G54630' => 'ath', 'AT3G05020' => 'ath', 'AT4G25050' => 'ath', 'AT5G27200' => 'ath', 'ATR0582G065' => 'atr', 'ATR0681G319' => 'atr', 'ATR0706G235' => 'atr', 'Atru.chr11.2418' => 'acertr', 'Atru.chr2.632' => 'acertr', 'Atru.chr4.2745' => 'acertr', 'Atru.chr7.1813' => 'acertr', 'AUR62000932' => 'cqu', 'AUR62005038' => 'cqu', 'BcaB04g19284' => 'bca', 'BcaB04g19653' => 'bca', 'BcaB04g21372' => 'bca', 'BcaB07g31097' => 'bca', 'BcaC01g04337' => 'bca', 'BcaC04g22022' => 'bca', 'BcaC04g23698' => 'bca', 'BcaC05g29984' => 'bca', 'BcaC05g29986' => 'bca', 'BcaC06g32840' => 'bca', 'BcaC07g38175' => 'bca', 'BcaC09g50814' => 'bca', 'BcaNung03995' => 'bca', 'BNapus_Darmor_BZH_scaffold_114p00290' => 'bna', 'BolC1t01977H' => 'bol', 'BolC1t05713H' => 'bol', 'BolC2t07350H' => 'bol', 'BolC3t16417H' => 'bol', 'BolC6t39808H' => 'bol', 'BolC7t45885H' => 'bol', 'BolC8t48597H' => 'bol', 'BolC9t53486H' => 'bol', 'BolC9t55367H' => 'bol', 'BraA01t01585Z' => 'bra', 'BraA03t14639Z' => 'bra', 'BraA05t22996Z' => 'bra', 'BraA08t34078Z' => 'bra', 'BraA09t36155Z' => 'bra', 'BraA09t37560Z' => 'bra', 'C01p20460' => 'bna', 'C03p41340' => 'bna', 'C05p62240' => 'bna', 'C06p47700' => 'bna', 'C07p53950' => 'bna', 'C09p05580' => 'bna', 'C09p24520' => 'bna', 'CAN.G223.5' => 'can', 'CAN.G256.7' => 'can', 'CAN.G843.27' => 'can', 'CANSAT54G2770' => 'cansat', 'CANSAT56G1768' => 'cansat', 'CANSAT78G0153' => 'cansat', 'CARHR055730' => 'chi', 'CARHR079340' => 'chi', 'CARHR185800' => 'chi', 'CARHR232450' => 'chi', 'Carub.0002s0895' => 'cru', 'Carub.0002s0904' => 'cru', 'Carub.0003s0426' => 'cru', 'Carub.0006s2531' => 'cru', 'Carub.0007s1598' => 'cru', 'Ca_00579_v3' => 'car', 'Ca_17582_v3' => 'car', 'Ca_21552_v3' => 'car', 'Cc00_g18410' => 'ccan', 'Cc03_g02430' => 'ccan', 'Cc07_g12250' => 'ccan', 'Cc11_g17510' => 'ccan', 'CDE01G0217' => 'cde', 'CDE02G4540' => 'cde', 'CDE06G0919' => 'cde', 'Cfa009432' => 'cfa', 'Cfa015501' => 'cfa', 'Ciclev10006180m.g' => 'ccl', 'Ciclev10010174m.g' => 'ccl', 'Ciclev10033025m.g' => 'ccl', 'CiPaw.01G153800' => 'cil', 'CiPaw.01G214600' => 'cil', 'CiPaw.02G087000' => 'cil', 'CiPaw.02G133300' => 'cil', 'CiPaw.05G103100' => 'cil', 'CiPaw.06G108200' => 'cil', 'ClCG02G016240' => 'cla', 'ClCG06G005420' => 'cla', 'ClCG06G018280' => 'cla', 'ClCG09G001210' => 'cla', 'COL.COLO4_13937' => 'col', 'COL.COLO4_21170' => 'col', 'COL.COLO4_36035' => 'col', 'Cpa.g.sc117.26' => 'cpa', 'Cpa.g.sc16.107' => 'cpa', 'Cpa.g.sc4.111' => 'cpa', 'Cpa.g.sc82.20' => 'cpa', 'Cre13.g577100' => 'cre', 'CsaV3_1G000160' => 'csa', 'CsaV3_2G004530' => 'csa', 'CsaV3_6G005690' => 'csa', 'CsaV3_7G034160' => 'csa', 'CSS0013626' => 'camsi', 'CSS0031867' => 'camsi', 'CSS0033984' => 'camsi', 'CSS0042766' => 'camsi', 'DCAR_002438' => 'dca', 'DCAR_024616' => 'dca', 'DCAR_026428' => 'dca', 'DCAR_027112' => 'dca', 'DCAR_030568' => 'dca', 'Dinv04280' => 'din', 'Dinv11224' => 'din', 'Dinv20399' => 'din', 'Dinv26583' => 'din', 'Dinv37841' => 'din', 'Dinv38331' => 'din', 'Dinv44432' => 'din', 'Duzib052G0874' => 'dzi', 'Duzib106G2029' => 'dzi', 'Duzib128G1526' => 'dzi', 'Duzib128G1724' => 'dzi', 'Duzib151G0162' => 'dzi', 'Duzib168G1696' => 'dzi', 'Duzib177G0726' => 'dzi', 'Duzib187G1045' => 'dzi', 'Duzib212G0038' => 'dzi', 'Duzib212G0858' => 'dzi', 'ECA232G0685' => 'eca', 'ECA232G3969' => 'eca', 'ECA233G5093' => 'eca', 'ECA238G4209' => 'eca', 'EL10Ac4g09243' => 'bvu', 'EL10Ac5g11309' => 'bvu', 'EL10Ac7g16606' => 'bvu', 'Eucgr.B01262' => 'egr', 'Eucgr.G01960' => 'egr', 'Eucgr.H03474' => 'egr', 'Eucgr.H03718' => 'egr', 'Eucgr.H03739' => 'egr', 'Eucgr.H03757' => 'egr', 'Eucgr.H03763' => 'egr', 'Eucgr.J02611' => 'egr', 'FAN01G3041' => 'fan', 'FAN02G1817' => 'fan', 'FAN03G2420' => 'fan', 'FAN04G0631' => 'fan', 'FAN05G0334' => 'fan', 'FAN05G3202' => 'fan', 'FAN06G3313' => 'fan', 'FAN06G4055' => 'fan', 'FAN07G1773' => 'fan', 'FAN08G0273' => 'fan', 'FAN09G2229' => 'fan', 'FAN09G4240' => 'fan', 'FAN10G0664' => 'fan', 'FAN12G0650' => 'fan', 'FAN12G2974' => 'fan', 'FAN13G0858' => 'fan', 'FAN14G3063' => 'fan', 'FAN17G2224' => 'fan', 'FAN18G0993' => 'fan', 'FAN22G2175' => 'fan', 'FvH4_4g17070' => 'fve', 'FvH4_5g09190' => 'fve', 'FvH4_6g04190' => 'fve', 'FvH4_7g04450' => 'fve', 'Glyma.03G242600' => 'gma', 'Glyma.05G201300' => 'gma', 'Glyma.07G042900' => 'gma', 'Glyma.08G008800' => 'gma', 'Glyma.10G158500' => 'gma', 'Glyma.13G214600' => 'gma', 'Glyma.15G098500' => 'gma', 'Glyma.16G011300' => 'gma', 'Glyma.19G240100' => 'gma', 'Glyma.20G230100' => 'gma', 'Gohir.A06G081200' => 'ghi', 'Gohir.A09G233100' => 'ghi', 'Gohir.A11G237500' => 'ghi', 'Gohir.A13G100800' => 'ghi', 'Gohir.A13G166200' => 'ghi', 'Gohir.D06G080800' => 'ghi', 'Gohir.D07G018350' => 'ghi', 'Gohir.D09G234200' => 'ghi', 'Gohir.D11G247900' => 'ghi', 'Gohir.D13G104400' => 'ghi', 'Gohir.D13G169100' => 'ghi', 'Gorai.001G019000' => 'gra', 'Gorai.006G257100' => 'gra', 'Gorai.007G264300' => 'gra', 'Gorai.010G094200' => 'gra', 'Gorai.013G116900' => 'gra', 'Gorai.013G192800' => 'gra', 'GSVIVG01004932001' => 'vvi', 'GSVIVG01016702001' => 'vvi', 'GSVIVG01017817001' => 'vvi', 'GSVIVG01021969001' => 'vvi', 'HanXRQChr08g0227701' => 'han', 'HanXRQChr09g0273951' => 'han', 'HanXRQChr14g0445471' => 'han', 'HanXRQChr16g0499561' => 'han', 'HanXRQChr17g0560841' => 'han', 'Haze_01051' => 'cav', 'Haze_12483' => 'cav', 'Haze_16088' => 'cav', 'Hma1.2p1_0078F.1_g040820' => 'hma', 'Hma1.2p1_0168F.1_g074080' => 'hma', 'Hma1.2p1_0643F.1_g194760' => 'hma', 'Hma1.2p1_0823F.1_g224560' => 'hma', 'HPP92_003152' => 'vpl', 'HPP92_025209' => 'vpl', 'HPP92_025277' => 'vpl', 'Hund07013' => 'sun', 'Hund10063' => 'sun', 'Hund21666' => 'sun', 'Lalb_Chr08g0237461' => 'lal', 'Lalb_Chr12g0196431' => 'lal', 'Lalb_Chr13g0303891' => 'lal', 'Lalb_Chr15g0087061' => 'lal', 'Lalb_Chr18g0055761' => 'lal', 'Lalb_Chr20g0118181' => 'lal', 'Lj3A811T82' => 'lonja', 'Lj4g0022032' => 'lja', 'Lj5A89T43' => 'lonja', 'Lj5g0027583' => 'lja', 'Lj6A668T52' => 'lonja', 'Lj9A536T70' => 'lonja', 'Lj9A536T71' => 'lonja', 'Lj9C485T6' => 'lonja', 'LjContig00389g0013894' => 'lja', 'Lsat_1_v5_gn_1_63361' => 'lsa', 'Lsat_1_v5_gn_2_66321' => 'lsa', 'Lsat_1_v5_gn_4_84020' => 'lsa', 'Lsat_1_v5_gn_4_91621' => 'lsa', 'Lsat_1_v5_gn_6_16040' => 'lsa', 'Manes.03G055600' => 'mes', 'Manes.03G190600' => 'mes', 'Manes.06G125400' => 'mes', 'Manes.08G125600' => 'mes', 'Manes.09G160200' => 'mes', 'Manes.15G017700' => 'mes', 'Manes.16G087900' => 'mes', 'Mapoly0009s0168' => 'mpo', 'Mapoly0030s0067' => 'mpo', 'MBI06_g11153_MAGBIO' => 'mbi', 'MBI10_g43288_MAGBIO' => 'mbi', 'MBI11_g43869_MAGBIO' => 'mbi', 'MBI14_g06396_MAGBIO' => 'mbi', 'MBI16_g34345_MAGBIO' => 'mbi', 'MBI18_g28677_MAGBIO' => 'mbi', 'MBI19_g04670_MAGBIO' => 'mbi', 'MBI19_g38001_MAGBIO' => 'mbi', 'MCO16G287' => 'mco', 'MD00G1052000' => 'mdo', 'MD06G1091300' => 'mdo', 'MD06G1091400' => 'mdo', 'MD06G1132700' => 'mdo', 'MD09G1176700' => 'mdo', 'MD12G1230300' => 'mdo', 'MD12G1230700' => 'mdo', 'MD12G1231000' => 'mdo', 'MD13G1174500' => 'mdo', 'MD15G1211200' => 'mdo', 'MD16G1176100' => 'mdo', 'MD17G1150100' => 'mdo', 'Medtr1g081920' => 'mtr', 'Medtr2g020360' => 'mtr', 'Medtr4g118750' => 'mtr', 'Medtr8g099920' => 'mtr', 'MELO3C004338.2' => 'cme', 'MELO3C021366.2' => 'cme', 'MELO3C024326.2' => 'cme', 'MELO3C026170.2' => 'cme', 'Migut.G00218' => 'egut', 'Migut.I00607' => 'egut', 'Migut.M01692' => 'egut', 'Migut.N00124' => 'egut', 'MSTRG.10048' => 'ama', 'MSTRG.21816' => 'ama', 'MSTRG.22858' => 'ama', 'MSTRG.24775' => 'ama', 'MSTRG.3958' => 'ama', 'Nitab4.5_0000235g0190' => 'nta', 'Nitab4.5_0000855g0240' => 'nta', 'Nitab4.5_0001459g0090' => 'nta', 'Nitab4.5_0001877g0020' => 'nta', 'Nitab4.5_0002046g0190' => 'nta', 'Nitab4.5_0002450g0060' => 'nta', 'Nitab4.5_0002794g0060' => 'nta', 'Nitab4.5_0003067g0010' => 'nta', 'Nitab4.5_0009936g0020' => 'nta', 'Nn3g16308' => 'nnu', 'Nn4g26041' => 'nnu', 'Oeu010968.1' => 'oeu', 'Oeu013652.1' => 'oeu', 'Oeu026207.1' => 'oeu', 'Oeu029277.1' => 'oeu', 'Os03g0856300' => 'osa', 'Os08g0549300' => 'osa', 'Os09g0539800' => 'osa', 'Os11g0521500' => 'osa', 'Os12g0534200' => 'osa', 'Peaxi162Scf00033g01724' => 'pax', 'Peaxi162Scf00314g00425' => 'pax', 'Peaxi162Scf00431g00312' => 'pax', 'Peaxi162Scf00861g00325' => 'pax', 'Peaxi162Scf01067g00112' => 'pax', 'PGR004G0212' => 'pgr', 'PGR031G0496' => 'pgr', 'PGR102G0576' => 'pgr', 'PGR119G0589' => 'pgr', 'PGSC0003DMG400010661' => 'stu', 'PGSC0003DMG400014253' => 'stu', 'PGSC0003DMG400030763' => 'stu', 'PGSC0003DMG400034344' => 'stu', 'Phvul.002G282800' => 'pvu', 'Phvul.003G100400' => 'pvu', 'Phvul.006G096600' => 'pvu', 'Phvul.006G160800' => 'pvu', 'Phvul.010G126500' => 'pvu', 'Potri.005G044800' => 'ptr', 'Potri.006G217800' => 'ptr', 'Potri.012G105300' => 'ptr', 'Potri.013G031300' => 'ptr', 'Potri.015G104500' => 'ptr', 'Potri.018G047201' => 'ptr', 'Pp3c14_24710' => 'ppa', 'Pp3c17_24100' => 'ppa', 'Pp3c17_24230' => 'ppa', 'PRCOL_00004879' => 'pco', 'Prupe.1G142900' => 'ppe', 'Prupe.1G204300' => 'ppe', 'Prupe.3G035800' => 'ppe', 'Prupe.5G143700' => 'ppe', 'Prupe.5G144100' => 'ppe', 'Prupe.6G335300' => 'ppe', 'Psat1g186960' => 'psa', 'Psat4g029440' => 'psa', 'Psat6g148160' => 'psa', 'Psat7g038920' => 'psa', 'PSO017G3577' => 'pso', 'PSO063G5623' => 'pso', 'PSO210G7264' => 'pso', 'PSO478G2250' => 'pso', 'PSO832G2041' => 'pso', 'PSO832G4237' => 'pso', 'QL02p023354' => 'qlo', 'QL03p000959' => 'qlo', 'QL03p049862' => 'qlo', 'QL06p007261' => 'qlo', 'RcHm_v2.0_Chr2g0104581' => 'rch', 'RcHm_v2.0_Chr2g0146771' => 'rch', 'RcHm_v2.0_Chr3g0452861' => 'rch', 'RcHm_v2.0_Chr4g0420871' => 'rch', 'RcHm_v2.0_Chr7g0188991' => 'rch', 'Rhsim02G0014100' => 'rsi', 'Rhsim04G0215700' => 'rsi', 'Rhsim08G0242100' => 'rsi', 'Rhsim12G0180300' => 'rsi', 'Sabra05G0041500' => 'sbr', 'Sabra12G0077700' => 'sbr', 'Sabra15G0124200' => 'sbr', 'SalBow1G5955' => 'sbo', 'SalBow2G3166' => 'sbo', 'SalBow3G1868' => 'sbo', 'SalBow3G2070' => 'sbo', 'SalBow5G0016' => 'sbo', 'SalBow5G2878' => 'sbo', 'Sc10g0010750' => 'sci', 'Sc10g0010840' => 'sci', 'Sc13g0003650' => 'sci', 'Sc19g0004920' => 'sci', 'Sed0006202' => 'sed', 'Sed0006579' => 'sed', 'Sed0007245' => 'sed', 'Sed0019593' => 'sed', 'Sed0023283' => 'sed', 'SEGI_08479' => 'sgi', 'SEGI_13053' => 'sgi', 'SEGI_20733' => 'sgi', 'SEGI_21967' => 'sgi', 'SGA_v2.0_scaffold142G35680' => 'sas', 'SGA_v2.0_scaffold40G15615' => 'sas', 'SGA_v2.0_scaffold57G20260' => 'sas', 'SGA_v2.0_scaffold89G27556' => 'sas', 'SHI18229' => 'shi', 'SMO143G0179' => 'smo', 'SMO143G0214' => 'smo', 'SMO147G0413' => 'smo', 'SMO364G0012' => 'smo', 'Solyc01g067730.3' => 'sly', 'Solyc02g038720.2' => 'sly', 'Solyc03g118410.3' => 'sly', 'Solyc06g054510.4' => 'sly', 'Sopen01g029680' => 'spe', 'Sopen03g037300' => 'spe', 'Sopen06g019580' => 'spe', 'Sp2g20440' => 'spa', 'Sp3g03850' => 'spa', 'Sp7g23040' => 'spa', 'SpUn0001_0010' => 'spa', 'TAR362G0229' => 'tar', 'TAR365G1181' => 'tar', 'TAR629G1738' => 'tar', 'TAR633G1675' => 'tar', 'TAR636G3460' => 'tar', 'THA.LOC104802818' => 'tha', 'THA.LOC104805837' => 'tha', 'THA.LOC104808037' => 'tha', 'THA.LOC104811562' => 'tha', 'THA.LOC104818660' => 'tha', 'THA.LOC104823741' => 'tha', 'THA.LOC104825036' => 'tha', 'Thecc.04G276300' => 'tca', 'Thecc.05G252900' => 'tca', 'Thecc.05G253800' => 'tca', 'Thecc.05G254000' => 'tca', 'Thecc.09G066600' => 'tca', 'Thhalv10005104m.g' => 'esa', 'Thhalv10021740m.g' => 'esa', 'Thhalv10023754m.g' => 'esa', 'Thhalv10023810m.g' => 'esa', 'Thhalv10024150m.g' => 'esa', 'Thhalv10026518m.g' => 'esa', 'TPR.G12955' => 'tpr', 'TPR.G13207' => 'tpr', 'TPR.G17628' => 'tpr', 'TPR.G2773' => 'tpr', 'TWI09G0976' => 'twi', 'TWI23G0639' => 'twi', 'TWI32G0332' => 'twi', 'TWI34G0596' => 'twi', 'TWI39G0694' => 'twi', 'TWI53G0572' => 'twi', 'TWI73G1296' => 'twi', 'unitig_22.g6333' => 'ugi', 'vmacro08208' => 'vma', 'vmacro08211' => 'vma', 'vmacro15267' => 'vma', 'vmacro16748' => 'vma', 'VMungo0251G0445' => 'vmu', 'VMungo0331G0272' => 'vmu', 'VMungo0540G1630' => 'vmu', 'VMungo0540G1813' => 'vmu', 'VMungo0720G2857' => 'vmu', 'VMungo1215G1373' => 'vmu', 'VMungo1383G1387' => 'vmu', 'Zm00001eb040040' => 'zma', 'Zm00001eb137740' => 'zma', 'Zm00001eb170330' => 'zma', 'Zm00001eb202830' => 'zma', 'Zm00001eb210480' => 'zma', 'Zm00001eb331920' => 'zma', 'Zm00001eb410630' => 'zma' ) $gf_id = 'HOM05D001276' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001276' ) $data_identifier = 'HOM05D001276' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 10, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 2, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 6, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 10, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 8, 'fan' => (int) 20, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 11, 'gra' => (int) 6, 'vvi' => (int) 4, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 6, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 12, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 9, 'nnu' => (int) 2, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 5, 'rsi' => (int) 4, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 5, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 4, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 4, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 7, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb410630' $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